Fibronectin binding protein-encoding DNA

ABSTRACT

The present invention relates to new recombinant DNA-molecules comprising nucleotide sequences of S. dysgalactiae encoding for at least one protein or polypeptide having fibronectin binding property.

This application is a continuation of application Ser. No. 07/973,551, filed Nov. 9, 1992, now abandoned; which is a continuation of application Ser. No. 07/352,949, filed May 17, 1989, now abandoned.

TECHNICAL FIELD

The present invention relates to fibronectin binding proteins and hybrid-DNA molecules, e.g., plasmids or phages containing at least one nucleotide sequence encoding for said proteins. Further the invention relates to micro-organisms containing such molecules and their use to produce said proteins, and the synthetic production of said proteins.

The object of the present invention is to obtain minimal fibronectin binding proteins.

A further object of the present invention is to obtain said proteins by means of genetic engineering techniques using e.g., a plasmid containing a nucleotide sequence encoding for the proteins.

A further object of the present invention is to obtain a possibility to prepare said proteins by means of chemical synthesis.

BACKGROUND OF THE INVENTION

WO-A1-85/05553 discloses bacterial cell surface proteins having fibronectin, fibrinogen, collagen, and/or laminin binding ability. Thereby it is shown that different bacteria have an ability to bind to fibronectin, fibrinogen, collagen and/or laminin. It is further shown that fibronectin binding protein from Staphylococcus aureus has a molecular weight of 165 kD, and/or 87 kD, whereby it is probable that the smaller protein is a part of the larger one.

Fibronectin is a large glycoprotein having a molecular weight of about 450 kD and having two similar subunits, which can have varying molecular sizes depending on a complex splicing pattern of the precursor mRNA. The protein is present in basement membranes, and connective tissue, but also in a soluble form in different body fluids, such as blood plasma (1). After the original discovery by Kuusela in 1978 that S. aureus binds to fibronectin (2) it has been shown that certain strains of other pathogenic bacteria, such as streptococci of different serological types (3), E. coli (4) and Salmonella (5) can bind to this protein (6).

Adhesion of pathogenic bacteria to surfaces is today a generally recognized concept in the discussions of wound pathogens using surface receptors to bind to different proteins on epithelium cell surfaces, in connective tissue matrix, and in wound crusts, such as e.g., fibronectin, fibrinogen, collagen and laminin. The problem is that these receptors are present in a relatively small amount on the bacterial cell surface, and that they are difficult to release. One feasible way in cases where the receptors consist of proteins is to clone the genes for the receptors in question to be able to prepare them in quantities which makes it considerably easier to study infections and the course of infections as well as proplylactic and therapeutic treatment of infections by wound pathogens.

Screening studies of different serological groups of streptococci, such as A, C, and G according to Lancefield (3) have shown that the strains tested can bind to different connective tissue proteins such as fibronectin, fibrinogen, collagen and laminin and different immunoglobulins (7,8) to a varying degree and with different specificity.

In order to further characterize fibronectin binding proteins from streptococci, particularly genes from Streptococcus dysgalactiae for such proteins have been cloned in E. coli. The fibronectin binding domains of these proteins have also been localized and properties and functions of proteins containing these domains will be discussed below.

DESCRIPTION OF THE PRESENT INVENTION

It has now surprisingly been shown possible to obtain hybrid-DNA molecules comprising nucleotide sequences of the genes coding for proteins or polypeptides having fibronectin binding properties. As evident from below the following nucleotide sequences are present in the plasmids, pSDF102, and pSDF203, respectively, which encode said proteins. ##STR1## whereby the smaller repetitive regions (cf. FIG. 3) in each gene above code for the peptides having fibronectin binding activity.

The invention further comprises a plasmid or phage comprising a nucleotide sequence coding for said fibronectin binding proteins.

The invention further comprises microorganisms containing at least one hydrid-DNA molecule according to above. Such micro-organisms have been deposited at the Deutsche Sammlung von Mikroorganismen under deposition number DSM 4614 (pSDF102) and DSM 4613 (pSDF203).

The invention further relates to a process for preparing fibronectin binding proteins comprising transfer of at least one hybrid-DNA molecule as set forth above into a microorganism, cultivating said microorganism in a culture medium, and isolating the protein thus formed in a manner known per se.

A further aspect of the present invention comprises a chemical synthesis of the fibronectin binding proteins, whereby amino acids attach to form peptides in which the order of amino acids is based upon said nucleotide sequences encoding said proteins. The synthesis starts from the C-terminal glycine, and aspartic acid, respectively, which are reacted stepwise with the appropriate amino acid, whereby they are finally reacted with glutamic acid, and glutamic acid, respectively, at the N-terminal end to form of the fibronectin binding peptide regions.

Appropriate amino acids can also be fused to said amino acid sequence such as the IgG binding region of protein A. The invention will be described more in detail as follows with reference to the Examples given, however, without being restricted thereto.

EXAMPLE 1 Construction of a gene bank of chromosomal DNA from Streptococcus dysgalactiae

Chromosomal DNA from Streptococcus dysgalactiae, strain S2, was prepared in accordance with the perchlorate method (9). The DNA was partially cleaved using Sau 3AI, was size fractionated on a 1% agarose gel, and the DNA fragment within the size range 3 to 9 kb were collected, electro eluated, and purified on a Nensorb (Du Pont) column.

The plasmid vector pUC18 was cleaved using Bam HI and was phosphatase treated. The partially cleaved and fractionated streptococcus-DNA was ligated with the cleaved pUC18 vector.. The ligation mixture was transformed to freeze competent E. coli, strain TG1, and was spread on LA plates containing ampicillin (50 μg/ml) and IPTG (0.1 mM), and 0.004% X-gal, called axiplates. White colonies were transferred to LA plates with ampicillin (50 μg/ml).

Screening of a gene bank for a fibronectin binding protein (FNBP)

The white colonies from the axi plates were picked using tooth picks to LA plates with ampicillin, 52 colonies per plate. In total 728 transformants were collected. These were screened with regard to fibronectin binding activity using a filter assay method according to below.

Transformants are picked from an axi-plates to LA plates with ampicillin, and the plates are incubated over night. From these plates the colonies are replicated over to new LA plates, and which are incubated at 37° C. over night. A nitro-cellulose filter is put onto each agarplate with grown out colonies. When the filters are completely moistened the colonies are attached by suction and the filters are carefully removed. The filters are exposed to chloroform vapor for 5 min, and are then washed, 3×10 min, 37° C. in a buffer solution consisting of 100 mM Tris-HCl pH 7.5, 0.05% Tween-40, and 150 mM NaCl. The filters are allowed to dry at room temperature for about 30 min. The filters are preincubated in 150 mM NaCl, 10 mM Tris-HCl pH 7.5, and 1.4% fat free milk powder, for 2 hrs at 37° C., or room temperature over night. The milk powder buffer has to be freshly prepared. ¹²⁵ I labelled fibronectin is added (about 30,000 cpm per filter), and the filters are incubated at room temperature over night. The filters are washed, 3×10 min at 37° C. using a solution of 0.05% Tween-40, and 150 mM NaCl, whereupon the filters are dried. An unexposed film is put thereon, and is exposed for 3 to 5 days. The film is developed and the clones which have bound to ¹²⁵ I-fibronectin are identified and isolated.

The filter screening assay showed 3 positive clones, which all were further analysed. The fibronectin binding ability was further determined in a competition assay (10). Lysate of the E. coli clones were prepared by lysing the bacteria using lysozyme (1 mg/ml) in a buffer solution consisting of 100 mM Tris-HCl pH 7.5, 150 mM NaCl, and 1 mM EDTA. The fibronectin binding activity was analysed by determining the ability of the lysates to compete with S. aureus, strain Cowan I (alternatively strain 8325-4), and S. dysgalactiae, strain S2, respectively, with regard to their ability to bind to the ¹²⁵ I-labelled 29 kD fragment of fibronectin. The test showed that it is possible to drive out the fibronectin binding to the two staphylococcal strains, as well as strain S2 of S. dysgalactiae when using lysates of E. coli clones containing the strepto-cocci DNA. Inversely the binding of the 29 kD fragment of fibronectin to S. dysgalactiae can be inhibited by adding a lysate of E. coli clone containing a gene for fibronectin binding protein of S. aureus.

Restriction mapping and subcloning

Plasmid-DNA of the three positive subclones from the filter assay, called pSDF100, pSDF200, and pSDF300 were prepared using the LiCl method (11) and determined to be 4.9 kb, 6.9 kb, and 6.5 kb, respectively, by cleavages using restriction enzymes and analysis on agarose gels. All three clones were cleaved using about 20 of the most common restriction enzymes, which recognizes a sequence of 6 nucleotides and starting from cleavage pattern restriction maps were drafted. Two of the clones, pSDF100, and pSDF300, were partly overlapping having a 3.9 kb sequence in common, and thus only one was selected for further studies. As pSDF100 had a higher fibronectin binding activity than pSDF300 the former was selected.

pSDF100 and pSDF200 were subcloned in order to identify more closely the regions encoding fibronectin binding activity. pSDF100 was cleaved using Bam HI, whereupon the plasmid was religated. This clone with the Bam HI-Barn HI fragment deleted was called pSDF101 and was positive. pSDF101 was further cleaved using XbaI, which gave 3 fragments, one mainly consisting of the pUC18 vector,. The other two XbaI-XbaI fragments were purified and inserted into the pUC18 vector. One of these fragments encodes fibronectin binding activity. This clone was called pSDF102. In the corresponding way subclones were constructed from pSDF200. The ClaI-SacI fragment deleted from pSDF200 gave a clone called pSDF201, and further the BglII-EcoRI fragment eliminated from pSDF201 gives pSDF202. Finally, the XhoI-EcoRI fragment has been deleted from pSDF202. This new clone was thereby obtained and was called pSDF203. All these new subclones are positive, i.e., they express fibronectin binding activity, cf. FIG. 1a and FIG. 1b.

Further subcloning by EcoIII digestion

In order to facilitate the nucleotide sequencing according to the dideoxymethod smaller subclones differing 150 to 200 base pairs in length are required in order to obtain overlapping DNA sequence. Exonucleas III digest one of the DNA strands from the 5' overhang, or from the blunt end, but leaves the 3' overhang. The single stranded DNA is then digested using S1-nuclease. This technique is used in the "Erase-a-Base" System Kit (Promega, Madison, USA) and makes it possible to construct series of subclones which differs in some hundreds of nucleotides in size. In cases of interest the fibronectin binding activity was tested, cf. Table 1 below.

Table 1

Inhibition assay in tubes

Assay mixture: 100 μ/l of lysate of E. coli clones containing streptococcal DNA clones (the bacteria were grown on LB+50 μg ampicillin+1 mM IPTG, washed, and concentrated to OD₅₄₀ =5.0) 100 μl Cowan I cells, heat killed, OD₅₄₀ =5.0 100 μl ¹²⁵ I labelled fibronectin, 8865 cpm 200 μl PBS+0.1% BSA

Incubation: 2 hrs, room temperature

Washing: Twice in PBS+0.1% BSA+0.05 % Tween

The results are evident from Table 1 below.

    ______________________________________                                                                       % binding in relation                            Lysate of                                                                               Dilution of Number   to control without                               subclone Lysate      of cpm   lysate                                           ______________________________________                                         Control  Without lysate                                                                             4430     100                                              pSDF102c10                                                                              undil        550     12.4                                                      10.sup.-2   3870     87.4                                             pSDF102c13                                                                              undil        200     4.5                                                       10.sup.-2   1440     32.5                                             pSDF102c9                                                                               undil        610     13.8                                                      10.sup.-2   3170     71.6                                             pSDF102c11                                                                              undil       1400     31.6                                                      10.sup.-2   3490     78.8                                             pSDF102c14                                                                              undil        630     14.2                                                      10.sup.-2   3220     72.7                                             pSDF102c18                                                                              undil       4030     91.0                                                      10.sup.-2   4300     97.1                                             pSDF203c3                                                                               undil        640     14.4                                                      10.sup.-2   2780     62.8                                             pSDF203c6                                                                               undil       2710     61.2                                                      10.sup.-2   4790     108                                              pSDF203c8                                                                               undil       3180     71.8                                                      10.sup.-2   3660     82.6                                             pSDF203c11                                                                              undil       3540     79.9                                                      10.sup.-2   3970     89.6                                             pSDF203c15                                                                              undil       3860     87.1                                                      10.sup.-2   4300     97.1                                             pSDF203c9                                                                               undil       4020     90.7                                                      10.sup.-2   4730     107                                              pSDF102  undil        200     4.5                                                       10.sup.-2   1050     23.7                                             pSDF203  undil        180     4.1                                                       10.sup.-2    950     21.4                                             TG1      undil       3690     83.3                                             ______________________________________                                    

Nucleotide sequencing

Subclones obtained after an exoIII digestion and other subclones were sequenced using the dideoxy method according to Gem Seq^(R) dsDNA Sequencing System (Promega Botech., Madison, USA)

Nucleotide sequencing of pSDF102 gave the following sequence: ##STR2## whereby the repetitive domains of the sequence ##STR3## encode a peptide having fibronectin binding activity.

The nucleotide sequencing of pSDF203 gave the following sequence ##STR4## whereby the repetitive domains of the sequence ##STR5## encode a peptide having fibronectin binding activity.

Southern blot hybridisation detects no homologies on DNA level between the genes for the fibronectin binding protein of S. aureus, and the corresponding genes from S. dysgalactiae. The competitive inhibition between the proteins from the respective species depends most probably on the fact that their binding sites in the fibronectin within the NH₂ terminal 29 kD fragment are close to each other and thereby sterically block the binding.

Western blot analyses of lysate of the two fibronectin binding E. coli clones studied indicate using ¹²⁵ I labelled fibronectin and autoradiography shows that subclone pSDF203 encodes a protein having a molecular weight of 70 kDa, and subclone pSDF102 a corresponding protein having a molecular weight of 110 kD.

The deduced amino acid sequences of the proteins or polypeptides from the above given nucleotide sequences encode for the following: ##STR6## respectively.

The present fibronectin binding proteins can be used in immunization, whereby the proteins, preferably in combination with a fusion protein in order to form a larger antigen to react upon, are injected in doses creating an. immunological reaction in the host mammal. Thus the fibronectin binding proteins can be used in vaccination of rumens to mastitis created by streptococcal infections.

Further, the fibronectin binding proteins can be used to block an infection in an open skin lesion. Wounds can be treated by using a suspension comprising the fibronectin binding protein. Thus the fibronectin binding proteins can be used to treat wounds, e.g., for blocking bacterial binding sites in fibronectin, or for immunization (vaccination). In the latter case the host produces specific antibodies which can protect against attachment by bacterial strains comprising such fibronectin binding proteins. Hereby the antibodies block the adherence of the bacterial strains to damaged tissue.

Examples of colonization and tissue damage are:

a) colonizing of wounds in skin and connective tissue, which wounds have been caused by a mechanical trauma, chemical damage, and/or thermical damage;

b) colonizing of wounds on muccus membranes such as in the mouth cavity, or in the mammary glands, urethra or vagina;

c) colonizing of connective tissue proteins, which have been exposed by minimal tissue damage (micro lesions) in connection with epithelium and endothelium (mastitis, heart valve infection, hip exchange surgery).

When using the present fibronectin binding proteins, prepared by means of hybrid-DNA technique, or synthesized, for immunization (vaccination) in mammals, including humans, the proteins, or polypeptides are dispersed in sterile isotonic saline solution, optionally while adding a pharmaceutically acceptable dispersing agent. Different types of adjuvants can further be used in order to sustain the release in the tissue, and thus expose the protein for a longer period of time to the immuno defense system of a body.

A suitable dose to obtain immunization is 0.5 to 5 μg of fibronectin binding protein per kg body weight and injection at immunization. In order to obtain durable immunization, vaccinations should be carried out at consecutive occasions with an interval of 1 to 3 weeks, preferably at three occasions. Adjuvants are normally not added when repeating the immunization treatment.

When using the present fibronectin binding proteins or polypeptides for local topical administration the protein is dispersed in an isotonic saline solution to a concentration of 25 to 250 μg per ml. The wounds are then treated with such an amount only to obtain a complete wetting of the wound surface. For an average wound thus only a couple of milliliters of solution are used in this way. After treatment using the protein solution the wounds are suitably washed with isotonic saline solution or another suitable wound treatment solution.

Further the fibronectin binding protein, or synthetized polypeptide of the present invention can be used to diagnose bacterial infections caused by S. dysgalactiae strains, whereby a fibronectin binding protein of the present invention is immobilized on a solid carrier, such as small latex or Sepharose^(R) beads, whereupon sera containing antibodies are allowed to pass and react with the fibronectin binding protein thus immobilized. The agglutination is then measured by known methods.

Further the fibronectin binding protein or polypeptide can be used in an ELISA test (Enzyme Linked Immuno Sorbent Assay; E Engvall, Med. Biol. 55, 193 (1977)). Hereby wells in a polystyrene microtitre plate are coated with the fibronectin binding protein and incubated over night at 4° C. The plates are then thoroughly washed using PBS containing 0.05% Tween 20, and dried. Serial dilutions of the patient serum made in PBS-Tween, are added to the wells and are incubated at 30° C. for 1.5 hrs. After rinsing anti-human IgG conjugated with an enzyme, or a horseradish peroxidase, or an alkaline phosphatase is added to the wells and further incubated at 30° C. for 1.5 hrs. During these incubations IgG from patient serum, and added antihuman IgG-enzyme conjugate, respectively, has been bound thereto. After rinsing, an enzyme substrate is added, p-nitrophosphate in case of an alkaline phosphatase, or orthophenylene diamine substrate (OPD) in case of a peroxidase has been used, respectively. The wells of the plates are then rinsed using a citrate buffer containing 0,055% OPD, and 0.005% H₂ O₂, and incubated at 30° C. for 10 min. The enzyme reaction is stopped by adding a 4N solution of H₂ SO₄ to each well. The color development is measured using a spectrophotometer.

Depending on the type of enzyme substrate used a fluoroscence measurement can be used as well.

Another method to diagnose S. dysgalactiae infections is by using the DNA gene probe method based on the nucleotide sequence for the fibronectin binding protein or part thereof. Thereby the natural or synthetic DNA sequence is attached to a solid carrier, such as a nitrocellulose filter, a nylon filter, or a polystyrene plate as mentioned above, by e.g., adding milk in the case of diagnosing a mastitis, to the surface. The DNA gene probe, optionally labelled enzymatically, or by a radioactive isotope, is then added to the solid surface plate comprising the DNA sequence, whereby the DNA gene probe attaches to the membrane associated sequence where appearing. The enzyme or radioactive isotope can readily be determined by known methods.

The above term fibronectin binding protein includes any of the polypeptide sequences as well, which constitute the minimal fibronectin binding site of the complete protein.

LEGENDS TO THE FIGURES

FIG. 1 Restriction map

FIG. 1a. Restriction map and subclones of the 5 kb insert from S. dysgalactiae in the pUC18-vector called pSDF100.

FIG. 1b. Restriction map and subclones of the 6.9 kb insert from S. dysgalactiae in the pUC18-vector called pSDF200. A. Restriction map of the clone. B. Different subclones constructed to determine the region in the gene which codes for fibronectin binding activity. The binding activity of the different gene products have been indicated. C. Subclones obtained after digestion with ExoIII of pSDF102, and pSDF203, respectively. Scale: 1 cm=100 bp. M is the part of the DNA sequence which encodes the membrane associated part of the protein (=COOH--terminal). Subclone p102c10 contains the 3' end of the gene (FIG. 1a). A₁, A₂ och A₃, and B₁, B₂, and B₃, respectively, denote repetitive domains of the sequences (cf. FIG. 3)

FIG. 2 Inhibition assay in tubes

Binding of ¹²⁵ I labelled fibronectin to cells of S. dysgalactiae S2, and S. aureus Cowan I, respectively, at the addition of lysates of E. coli-clones. The percentage values given are related to the binding of ¹²⁵ I labelled fibronectin to cells in the absence of lysate. As a negative control a lysate of E. coli TG1 with pUC18-vector without insert was used, which had no influence on the binding of the cells to fibronectin. E. coli clone 015 contains a gene from S. aureus encoding for fibronectin binding activity.

FIGS. 3a and 3b show repetitive sequences of pSDF102 and pSDF203.

FIG. 4 shows the nucleotide and deduced amino acid sequences of pSDF102

FIG. 5 shows the nucleotide and deduced amino acid sequences of pSDF203

References

1. Hymes, R. O. (1985) Annu. Rev. Cell Biol. 1, 67-90.

2. Kuusela, P. (1978) Nature 276, 718-720.

3. Switalski, L. et al (1982) Eur. J. Clin. Microbiol. 1, 381-387.

4. Froman, G. et al. (1984) J. Biol. Chem. 259, 14899-14905.

5. Baloda, S. B. et al (1985) FEMS Microbiol. Lett. 28, 1-5.

6. Wadstrom, T. et al (1985) In Jackson, G. J. (ed), Pathogenesis of Infection, Springer Verlag, Berlin, Heidelberg, New York, Tokyo, p p. 193-207.

7. Lopes, J. D. et al (1985) Science 229, 275-277.

8. Langone, I. I. (1982) Adv. Immunol. 32, 157-252.

9. Marmur, J. (1961) J. Mol. Biol. 3, 208-218.

10. Flock, J.-I. et al (1987) The EMBO Journal 6, 2351-2357.

11. Monstein, H.-J. et al (1986) Biochem. Int. 12, 889-896. 

We claim:
 1. Plasmid pSDF102 as contained in the E. coli TG1 strain, having the deposit number DSM
 4614. 2. Plasmid pSDF203 as contained in the E. cOli TG1 strain, having the deposit number DSM
 4613. 3. Substantially pure DNA encoding a fibronectin binding protein from S. dysgalactiae having the following sequence ##STR7##
 4. An E. coil microorganism transformed by the DNA molecule according to claim
 3. 5. An E. coli plasmid comprising the nucleotide sequence according to claim
 3. 6. An E. coli comprising a plasmid according to claim
 5. 7. An E. coli bacteriophage comprising the nucleotide sequence according to claim
 3. 8. An E. coli comprising a bacteriophagc according to claim
 7. 